After World War II, are all German aircraft manufacturers, including Junk and Messerschmitt, partly in East Germany and partly in West Germany?

Yes, Alado was dissolved.

Messerschmitt (formerly Bavarian Aircraft Factory, not Bavarian Machinery Factory (BMW)), Fokker Woolf, Henkel, Dornier and Juncker were all merged, and now they should be EADS, and later they were renamed Airbus Group. After the war, Gotha returned to its old business, producing trams and light rail vehicles in East Germany.